Protein folding kinetics under force from molecular simulation

Despite a large number of studies on the mechanical unfolding of proteins, there are still relatively few successful attempts to refold proteins in the presence of a stretching force. We explore refolding kinetics under force using simulations of a coarse-grained model of ubiquitin. The effects of force on the folding kinetics can be fitted by a one-dimensional Kramers theory of diffusive barrier crossing, resulting in physically meaningful parameters for the height and location of the folding activation barrier. By comparing parameters obtained from pulling in different directions, we find that the unfolded state plays a dominant role in the refolding kinetics. Our findings explain why refolding becomes very slow at even moderate pulling forces and suggest how it could be practically observed in experiments at higher forces.     

Thermoresponsive behavior of charged <Emphasis Type="Italic">N</Emphasis>-isopropylacrylamide-based hydrogels containing gold nanostructures

We report the synthesis of N-isopropylacrylamide-based hydrogels containing either an anionic (acrylic acid) or cationic ([2-(acryloyloxy)ethyl]trimethylammonium chloride) co-monomer. These hydrogels were cross-linked with a cleaveable (N,N′-cystaminebisacrylamide) and/or inert (N,N′-methylenebisacrylamide) molecule in four combinations. Gold nanostructures were then synthesized within these hydrogel matrices by in situ reduction of a metal ion precursor. The resulting eight nanocomposites and their non-gold-containing (native) analogs were characterized with several analytical methods. UV–visible and infrared spectroscopy revealed differences among the samples based largely on the concentration and identity of cross-linking agent. Equilibrium swelling masses and phase transition behavior point to differences among samples on charge of the hydrogel backbone, cross-linker type, and presence or absence of gold nanostructures. A molecular level explanation for these observations is described.     

Effects of electric fields on proton transport through water chains

Molecular dynamics simulations on quantum energy surfaces are carried out to study the effects of perturbing electric fields on proton transport (PT) in protonated water chains. As an idealized model of a hydrophobic cavity in the interior of a protein the water molecules are confined into a carbon nanotube (CNT). The water chain connects a hydrated hydronium ion (H3O+) at one end of the CNT and an imidazole molecule at the other end. Without perturbing electric fields PT from the hydronium proton donor to the imidazole acceptor occurs on a picosecond time scale. External perturbations to PT are created by electric fields of varying intensities, normal to the CNT axis, generated by a neutral pair of charges on the nanotube wall. For fields above approximately 0.5 VA, the hydronium ion is effectively trapped at the CNT center, and PT blocked. Fields of comparable strength are generated inside proteins by nearby polar/charged amino acids. At lower fields the system displays a rich dynamic behavior, where the excess charge shuttles back and forth along the water chain before reaching the acceptor group on the picosecond time scale. The effects of the perturbing field on the proton movement are analyzed in terms of structural and dynamic properties of the water chain. The implications of these observations on PT in biomolecular systems and its control by external perturbing fields are discussed.     

Pair diffusion, hydrodynamic interactions, and available volume in dense fluids

We calculate the pair diffusion coefficient D(r) as a function of the distance r between two hard sphere particles in a dense monodisperse fluid. The distance-dependent pair diffusion coefficient describes the hydrodynamic interactions between particles in a fluid that are central to theories of polymer and colloid dynamics. We determine D(r) from the propagators (Green's functions) of particle pairs obtained from molecular dynamics simulations. At distances exceeding ~3 molecular diameters, the calculated pair diffusion coefficients are in excellent agreement with predictions from exact macroscopic hydrodynamic theory for large Brownian particles suspended in a solvent bath, as well as the Oseen approximation. However, the asymptotic 1/r distance dependence of D(r) associated with hydrodynamic effects emerges only after the pair distance dynamics has been followed for relatively long times, indicating non-negligible memory effects in the pair diffusion at short times. Deviations of the calculated D(r) from the hydrodynamic models at short distances r reflect the underlying many-body fluid structure, and are found to be correlated to differences in the local available volume. The procedure used here to determine the pair diffusion coefficients can also be used for single-particle diffusion in confinement with spherical symmetry.     

Pharmacoinformatics-based identification of transmembrane protease serine-2 inhibitors from Morus Alba as SARS-CoV-2 cell entry inhibitors

Molecular Diversity - Transmembrane protease serine-2 (TMPRSS2) is a cell-surface protein expressed by epithelial cells of specific tissues including those in the aerodigestive tract. It helps the...     

New thermodynamic/electrostatic models of adsorption and tension equilibria of aqueous ionic surfactant mixtures: application to sodium dodecyl sulfate/sodium dodecyl sulfonate systems

The nonideal adsorbed solution (NAS) theory has been formally extended to adsorption at the air/water interface from aqueous mixtures of ionic surfactants, explicitly accounting for the surface potential of the adsorbed monolayer with the Gouy-Chapman theory. This new ionic NAS (iNAS) theory is thermodynamically consistent and, when coupled to a micellization model, is valid for concentrations below and above the mixed cmc. Counterion binding is incorporated into the model using two fractional binding parameters, beta(sigma) for the adsorbed monolayer and beta(m) for the micelles. The regular solution theory is used to model the nonideal interactions within the adsorbed monolayer and within the mixed micelles. New tension data for an equimolar mixture of sodium dodecyl sulfate (SDS) and sodium dodecyl sulfonate (SDSn) at two salinities fit this model well when mixing is ideal. The total surface densities, the surface compositions, and the surface potentials for the mixed monolayers are calculated. When there is no added salt, at total surfactant concentrations below the mixed cmc, the adsorbed monolayer is enriched in SDSn, but at total concentrations at and above the mixed cmc, the adsorbed monolayer is nearly an equimolar mixture. In the presence of 100 mM NaCl, the adsorbed monolayer is nearly an equimolar mixture, independent of the total surfactant concentration.     

Lowest optical excitations in molecular crystals: bound excitons versus free electron-hole pairs in anthracene

By solving the Bethe-Salpeter equation for the electron-hole Green function for crystalline anthracene we find the lowest absorption peak generated by strongly bound excitons or by a free electron-hole pair, depending on the polarization direction being parallel to the short or the long molecular axis, respectively. Both excitations are shifted to lower energies by pressure. The physical difference of these excitations is apparent from the electron-hole wave functions. Our findings are a major contribution to solve the long-standing puzzle about the nature of the lowest optical excitations in organic materials.     

Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome p450cam

Proton-transfer reactions form an integral part of bioenergetics and enzymatic catalysis. The identification of proton-conducting pathways inside a protein is a key to understanding the mechanisms of biomolecular proton transfer. Proton pathways are modeled here as hydrogen bonded networks of proton-conducting groups, including proton-exchanging groups of amino acid side chains and bound water molecules. We focus on the identification of potential proton-conducting pathways inside a protein of known structure. However, consideration of the static structure alone is often not sufficient to detect suitable proton-transfer paths, leading, for example, from the protein surface to the active site buried inside the protein. We include dynamic fluctuations of amino acid side chains and water molecules into our analysis. To illustrate the method, proton transfer into the active site of cytochrome P450cam is studied. The cooperative rotation of amino acids and motion of water molecules are found to connect the protein surface to the molecular oxygen. Our observations emphasize the intrinsic dynamical nature of proton pathways where critical connections in the network may be transiently provided by mobile groups.